GPCRmd

GPCRmd Workbench

Help

Indicate what you want to display in your molecular representation using the selection options of the GPCRmd Viewer.

You can choose one of the selections we propose or define a new one (Customized selection option) using the NGL selection language.

Visualization and trajectory sharing powered by NGL Viewer and MDsrv.

The hydrogen bonding network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.

Mutant and variant information obtained from GPCRdb and gnomAD.

Mouse controls:

Left button hold and move: rotate camera around center.

Left button click: pick atom or distance.

Middle button hold and move: zoom camera in and out.

Middle button click: center camera on atom.

Right button hold and move: translate camera in screen plane.

For more information, see the docs.

GPCRmd Viewer

Beta-1 adrenergic receptor in complex with R-dobutamine (2Y00.B)

Simulation report and files

Selection

Structure selection

Quick selection

Show within Å of

Custom selection

Input your selection using the NGL selection language. Generic GPCR residue numbering can also be used (more info here).

GPCRmd Toolkit

Interaction network

Hydrogen bonds:

GetContacts criteria

Interaction frequencies

Hydrogen bonds

Trajectory:

Frames:

All

From to

Selection:

Do not include hydrogen bonds between neighbours

All hydrogen bonds

Only side chain hydrogen bonds

Threshold: %

Ligand receptor contacts

Compute interaction between GPCR and

In trajectory:

Stride:

Threshold: Å

Consider

Salt bridges

Trajectory:

Frames:

All

From to

Threshold: %

Distance

Select distances from the viewer by clicking on the atoms. Afterwards, import your selections by clicking at the import button (). You can also manually introduce the atom indices.

Compute distance between and

In trajectory:

Stride:

RMSD

Trajectory:

Frames:

All

From to

Stride:

Reference: frame from trajectory

Selection:

Protein alpha carbons

Protein CA, CB, C, N, O

Non-hydrogen protein atoms

All protein atoms

(R)-DOBUTAMINE

Experimental density map

Quick selection

Custom selection

Selection settings

× Make a selection to display the map.

Apply default representations

	2fo-fc	fo-fc
Display map
Map color		Pos Neg
Map style
ISO level	1.5	3
Zoom	0

Water distribution

Volume distribution


Display map	Loading...
Map style
Opacity	0.5
Smoothness	1
ISO level	0.3
Show Polar residues
Show waters within	Å of protein

Dynamic pharmacophores

Display:

Ligand pharmacophores

Receptor pharmacophores

Interaction type:

Color pattern:

Tunnels and channels

	Clusters	Highest throughput

Style		-
c1
c2
c3
c4
c5
c6
c7
c8
c9
c10
c11
c12
c13

Pockets

Show nearby residues?

Smoothing window size:

Pocket number	Color	Mean volume	Avg. Polarity	Avg. Hydroph. Density	Avg. Hydroph. Score	Druggability %

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